[W]e have abundant signs of recent positive selection in the genome, but those signs are nearly all very recent partial sweeps in different human populations. Complete sweeps and near-complete sweeps are indeed few, suggesting that there was relatively little directional adaptive evolution associated with the "origin of modern humans." Measuring by genetic change, agriculture was many times more important than the appearance of modern humans throughout the world. The important point with respect to archaic humans is that there are precious few genetic changes shared by all (or even most) humans today, that are not also shared with Neandertals, Denisovans, or plausible other archaic human groups (such as archaic Africans).

That of course follows from the fact that a fraction of today's gene pool actually comes from those ancient groups. Their variation is (by and large) human variation.

I'm not even sure what this high level terminology describes in terms of on the ground measurable facts. But something to look into...not sure if the paper cited is a good start, I assume not, I'm looking for something more quantitative.

The appearance of anatomically modern humans in Europe and the nature of the transition from the Middle to Upper Palaeolithic are matters of intense debate. Most researchers accept that before the arrival of anatomically modern humans, Neanderthals had adopted several ‘transitional’ technocomplexes. Two of these, the Uluzzian of southern Europe and the Châtelperronian of western Europe, are key to current interpretations regarding the timing of arrival of anatomically modern humans in the region and their potential interaction with Neanderthal populations. They are also central to current debates regarding the cognitive abilities of Neanderthals and the reasons behind their extinction1, 2, 3, 4, 5, 6. However, the actual fossil evidence associated with these assemblages is scant and fragmentary7, 8, 9, 10, and recent work has questioned the attribution of the Châtelperronian to Neanderthals on the basis of taphonomic mixing and lithic analysis11, 12. Here we reanalyse the deciduous molars from the Grotta del Cavallo (southern Italy), associated with the Uluzzian and originally classified as Neanderthal13, 14. Using two independent morphometric methods based on microtomographic data, we show that the Cavallo specimens can be attributed to anatomically modern humans. The secure context of the teeth provides crucial evidence that the makers of the Uluzzian technocomplex were therefore not Neanderthals. In addition, new chronometric data for the Uluzzian layers of Grotta del Cavallo obtained from associated shell beads and included within a Bayesian age model show that the teeth must date to ~45,000–43,000 calendar years before present. The Cavallo human remains are therefore the oldest known European anatomically modern humans, confirming a rapid dispersal of modern humans across the continent before the Aurignacian and the disappearance of Neanderthals.

May 12, 2010

Last week's issue of Science touches on one of my favorite topics (about which I know far too little): The Origins of C4 Grasslands. There's not too much new in the survey, basically a call for more research, but it lays out some of the background.

Photosynthesis is the fundamental biological process that transformssolar energy into the chemical fuel for life by generating sugarsfrom water and CO2. The ancestral pathway (C3
photosynthesis)evolved in a CO2-rich atmosphere
more than 2800 million yearsago (Ma), but depletion of
atmospheric CO2 about 30 Ma has reducedthe
efficiency and rate of carbon uptake in many terrestrialplants,
especially under high temperatures and water deficits(1).
This limitation has been alleviated through the convergentevolution
of C4 photosynthesis in more than 45 independent floweringplant lineages (1).
C4 photosynthesis is a coordinated systemof
anatomical and physiological traits that concentrate CO2around the C3 photosynthetic machinery, through the
use of asolar-powered biochemical cycle. The emergence of
ecosystemsdominated by C4 species has transformed
the biosphere; althoughcomprising only 3% of vascular plant
species (1),
they accountfor some 25% of terrestrial photosynthesis (2).

Sixty percent of C4 species are grasses, dominating
warm-climategrasslands and savannas (Fig.
1A), where their high rates offoliage production sustain
Earth’s highest levels of herbivoreconsumption (3).
Stable carbon isotopic data (13C)
collectedover the past 20 years document a worldwide
expansion of C4grasslands through the
displacement of C3the Late
Miocene and Pliocene (3 to 8 Ma) (4).
This was a dramaticevent of biome evolution in Earth’s
history, outpacingthe rise to dominance of flowering plants
during the Cretaceousby one order of magnitude (5),
but its drivers are still debated. ...

Today’s C4 grasses are mostly confined to low latitudesand
altitudes, whereas C3 species dominate at higher latitudesand elevations (Fig.
1A). These patterns correlate best withtemperature, with
several classic studies (6)
showing the relationshipon every continent. Explanations of
these gradients have traditionallyfocused on fundamental
physiological differences between C3and C4
photosynthesis. At high temperatures and low atmosphericCO2,
the key C3 photosynthetic enzyme rubisco fails to completelydistinguish CO2 and O2. The process of O2
uptake leads to photorespirationin C3 plants,
resulting in net losses of 40% of
photosyntheticcarbon in today’s low-CO2
atmosphere (1).
C4 photosynthesissuppresses photorespiration by
concentrating CO2 internally,but this comes with
an energetic cost, which exceeds the photorespiratorycosts
of C3 photosynthesis at high CO2 and low
temperatures(7,
8).
All else being equal, C4 grasses will therefore outperformC3 grasses below a critical threshold in CO2,
the level of whichdepends on growing-season temperature (Fig.
1B) (7,
8).
By saturatingrubisco with CO2, the C4
pathway also allows the enzyme to achievemaximum catalytic
rates under high-light conditions (9);
conversely,the overall C4 advantage is often
lost in shaded forest understories,where cool conditions
improve the quantum efficiency in C3 species(7).

This functional model forms the central basis for understandingthe
current distribution of C4 grasses and grasslands (Fig.
1A) and the general absence of C4 grasses from forest
understoryhabitats (10).
It explains glacial-interglacial cycles of C4grassland
expansion and contraction (10)
and underpins forecastsof future impacts of global change
on Earth’s C3-C4 balance(11).
The extension of this model to the geological past generatesthe
hypothesis that declining atmospheric CO2 drove the
displacementof C3 plants by C44,
8,
10).
Because lower temperaturesreduce the crucial CO2
threshold for a C4(Fig.
1B), C4 grasslands should have appeared first in the
tropicsat 350 to 550 parts per million (ppm) CO2
and then spread tohigher latitudes as CO210). ...

Recent phylogenetic reconstructions show that C4
photosynthesishas evolved multiple times in grasses (16,
17).
Time-calibrationof these phylogenies using fossilized grass
pollen and inflorescencesplaces the earliest probable
origin in the Early Oligocene (~30to 32 Ma) (Fig. 2)
and suggests that subsequent origins arosein clusters (for
example, in the Middle Miocene). This timinghas led
researchers to hypothesize that the Early Oligocenedrop in
CO2 triggered evolution of the C4 pathway (16,
17).However, the proposal is challenged by the discovery of LateCretaceous microscopic plant silica (phytoliths) diagnosticof
grasses (Fig. 2),
suggesting that this lineage may be mucholder than
previously thought (18).
A recalibration with thesefossils would date the earliest C4
grasses to the Middle Eocene(17),
a time of warm equable climates and probably of high CO2(Fig. 2).
Even more controversial are 13C
records from leaf-waxmolecules (n-alkanes) in marine
sediments, indicating that C4photosynthesis
existed in Cretaceous land plants (19),
albeitnot necessarily in grasses.
New paleontological evidence also reveals crucial informationabout
the Miocene environments that preceded C4 grasslands.Rather
than being forested, as initially thought (20),
it nowappears that landscapes were relatively open. The
evolutionof ungulate grazers or mixed feeders (feeding on
grasses andbroad-leaved plants) and pollen data (21)
supplemented by new,phytolith-based reconstructions of
vegetation (22)
documentthe emergence of savannas or woodlands with
predominantly C3grasses in the Early-Middle
Miocene (11 to 24 Ma), several millionyears before C4
grasslands spread (Fig. 3).
This vegetationshift is evident in all of the studied
cases, although its timingand pace seem to have varied among
regions (Fig. 3).

May 6, 2010

We have 1-4%
Neanderthal DNA in non-African (and less so in African) modern humans. Not quite sure I
understand this result, I'm surprised, I had sort of assumed that lack
of Neanderthal mDNA in modern humans implied no significant Neanderthal
DNA in homo sapiens due to lack of interbreeding. But that's selection:
mDNA didn't survive selection, but seemingly lots of nuclear DNA did
because it conferred selective advantage (plus some random drift).

Also,
how is this 1%+ DNA fraction measured...doesn't this raise the question
of significant African vs. non-African genetic difference? Ah, it's
1-4% Neanderthal ancestry, but there are lots of common genes between
the two (sub)species, so the contribution of Neanderthal genes to
African and non-African genetic differences is much less (see below). And there may be
Neanderthal gene flow back to Africa. [Update #1: ah, it's 1-4% excess Neanderthal ancestry for non-Africans compared to Africans. Again, depends on some modeling assumptions.]

Mutations
in several genes in Table 3
have been associated withdiseases affecting cognitive
capacities. DYRK1A, which liesin the Down syndrome
critical region, is thought to underliesome of the cognitive
impairment associated with having threecopies of chromsome
21 (64).
Mutations in NRG3 have been associatedwith
schizophrenia, a condition that has been suggested to affecthuman-specific
cognitive traits (65,
66).
Mutations in CADPS2have been implicated in autism (67),
as have mutations in AUTS2(68).
Autism is a developmental disorder of brain function inwhich
social interactions, communication, activity, and interestpatterns
are affected, as well as cognitive aspects crucialfor human
sociality and culture (69).
It may thus be that multiplegenes involved in cognitive
development were positively selectedduring the early history
of modern humans.

One gene of interest may be RUNX2
(CBFA1). It is the only
genein the genome known to cause cleidocranial dysplasia,
whichis characterized by delayed closure of cranial sutures,
hypoplasticor aplastic clavicles, a bell-shaped rib cage,
and dental abnormalities(70).
Some of these features affect morphological traits forwhich
modern humans differ from Neandertals as well as otherearlier
hominins. For example, the cranial malformations seenin
cleidocranial dysplasia include frontal bossing, i.e., aprotruding
frontal bone. A more prominent frontal bone is afeature
that differs between modern humans and Neandertals aswell as
other archaic hominins. The clavicle, which is affectedin
cleidocranial dysplasia, differs in morphology between modernhumans
and Neandertals (71)
and is associated with a differentarchitecture of the
shoulder joint. Finally, a bell-shaped ribcage is typical of
Neandertals and other archaic hominins. Areasonable
hypothesis is thus that an evolutionary change inRUNX2
was of importance in the origin of modern humans and thatthis
change affected aspects of the morphology of the upperbody
and cranium.

One of the really exciting aspects of this work is that both Green
and colleagues and Burbano and colleagues look for things that all
humans today share but Neandertals lack.

You might call these "the genes that make us modern," although
functionally we have little idea what any of them do.

Both papers show one thing that is extremely interesting: There
aren't very many such genetic changes.

Burbano and colleagues put together a microarray including all the
amino acid changes inferred to have happened on the human lineage. They
used this to genotype the Neandertal DNA, and show that out of more than
10,000 amino acid changes that happened in human evolution, only 88 of
them are shared by humans today but not present in the Neandertals.

That's amazingly few.

Green and colleagues did a similar exercise, except they went looking
for "selective sweeps" in the ancestors of today's' humans. These are
regions of the genome that have an unusually low amount of incomplete
lineage sorting with Neandertals, and therefore represent shallow
genealogies for all living people. They identify 212 regions that seem
to be new selected genes present in humans and not in Neandertals. This
number is probably fairly close to the real number of selected changes
in the ancestry of modern humans, because it includes non-coding changes
that might have been selected.

Again, that's really a small number. We have roughly 200,000-300,000
years for these to have occurred on the human lineage -- after the
inferred population divergence with Neandertals, but early enough that
one of these selected genes could reach fixation in the expanding and
dispersing human population. That makes roughly one selected
substitution per 1000 years.

Which is more or less the rate that we infer by comparing humans and
chimpanzees. What this means is simple: The origin of modern humans was
nothing special, in adaptive terms. To the extent that we can see
adaptive genetic changes, they happened at the basic long-term rate that
they happened during the rest of our evolution.

Now from my perspective, this means something even more interesting.
In our earlier work, we inferred a recent acceleration of human
evolution from living human populations. That is a measure of the number
of new selected mutations that have arisen very recently, within the
last 40,000 years. And most of those happened within the past 10,000
years.

In that short time period, more than a couple thousand selected
changes arose in the different human populations we surveyed. We
demonstrated that this was a genuine acceleration, because it is much
higher than the rate that could have occurred across human evolution,
from the human-chimpanzee ancestor.

What we now know is that this is a genuine acceleration compared to
the evolution of modern humans, within the last couple hundred thousand
years.

Our recent evolution, after the dispersal of human populations across
the world, was much faster than the evolution of Late Pleistocene
populations. In adaptive terms, it is really true -- we're more
different from early "modern" humans today, than they were from
Neandertals. Possibly many times more different.

Greece, UK election -- results so far are weird enough that I cannot tell who will form the government --, biggest intraday US stock plunge in history, European interbank credit issues (!), and more...can complain it isn't interesting. Best year since 1989? I am a big believer in the slow burn theory of events...sort of like 1931.

I'm offended by the unenlightened 'why should we pay?' view of the vast majority of the German public...it's pay now or loose more, probably sooner than later. Better central banking would be even better...how about ECB bond purchases and a commitment to getting the price level up 5% (i.e. no interest rate increases until the price level is up 5%)?